1 ;;;; -*- Mode: Lisp; Syntax: ANSI-Common-Lisp; Base: 10; Package: umlisp -*-
2 ;;;; *************************************************************************
3 ;;;; FILE IDENTIFICATION
5 ;;;; Name: sql-classes.lisp
6 ;;;; Purpose: Routines for reading UMLS objects from SQL database
7 ;;;; Author: Kevin M. Rosenberg
10 ;;;; This file, part of UMLisp, is
11 ;;;; Copyright (c) 2000-2010 by Kevin M. Rosenberg, M.D.
13 ;;;; UMLisp users are granted the rights to distribute and use this software
14 ;;;; as governed by the terms of the GNU General Public License.
15 ;;;; *************************************************************************
20 (defvar *current-srl* nil)
23 (defun set-current-srl (srl)
24 (setq *current-srl* srl))
26 (defmacro query-string (table fields srl where-name where-value
27 &key (lrl "KCUILRL") single distinct order like limit
29 (let* ((%%fields (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
30 (if distinct "DISTINCT " "") fields table))
31 (%%order (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}"
34 (%%lrl (format nil " AND ~:@(~A~)<=" lrl))
35 (%%where (when where-name
36 (format nil " WHERE ~:@(~A~)~A" where-name
37 (if like " like " ""))))
38 (%filter (gensym "FILTER-"))
39 (%single (gensym "SINGLE-"))
40 (%limit (gensym "LIMIT-")))
41 `(let ((,%limit ,limit)
47 ,@(when %%where (list %%where))
49 `((typecase ,where-value
52 (concatenate 'string "='" (prefixed-fixnum-string ,where-value #\0 10) "'"))
54 (concatenate 'string "='" (write-to-string ,where-value) "'"))
58 (format nil ,(if like "'%~A%'" "='~A'") ,where-value)))))
59 (if ,%filter (concatenate 'string
60 ,(if %%where " AND " " WHERE ")
62 (if ,srl (concatenate 'string ,%%lrl (write-to-string ,srl)) "")
63 ,@(when %%order (list %%order))
65 ((and ,%single ,%limit)
66 (error "Can't set single (~S) and limit (~S)" ,%single ,%limit))
70 (format nil " LIMIT ~D" ,%limit))
74 (defun query-string-eval (table fields srl where-name where-value
75 &key (lrl "KCUILRL") single distinct order like limit filter)
76 (when single (setq limit 1))
79 (format nil "SELECT ~A~{~:@(~A~)~^,~} FROM ~:@(~A~)"
80 (if distinct "DISTINCT " "") fields table)
81 (if where-name (format nil " WHERE ~:@(~A~)" where-name) "")
88 (if like " LIKE '%~A%'" "='~A'")))
91 (if filter (concatenate 'string " AND " filter) nil)
92 (if srl (format nil " AND ~:@(~A~)<=~D" lrl srl) "")
93 (if order (format nil " ORDER BY ~{~:@(~A~) ~(~A~)~^,~}" order) "")
94 (if limit (format nil " LIMIT ~D" limit) "")))
97 (defmacro umlisp-query (table fields srl where-name where-value
98 &key (lrl "KCUILRL") single distinct order like
99 limit filter (query-cmd 'mutex-sql-query))
100 "Query the UMLisp database. Return a list of umlisp objects whose name
101 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
103 (query-string ,table ,fields ,srl ,where-name ,where-value
104 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like
105 :filter ,filter :limit ,limit)))
107 (defmacro umlisp-query-eval (table fields srl where-name where-value
108 &key (lrl "KCUILRL") single distinct order like
110 "Query the UMLisp database. Return a list of umlisp objects whose name
111 is OBJNAME from TABLE where WHERE-NAME field = WHERE-VALUE with FIELDS"
113 (query-string-eval ,table ,fields ,srl ,where-name ,where-value
114 :lrl ,lrl :single ,single :distinct ,distinct :order ,order :like ,like
115 :filter ,filter :limit ,limit)))
117 ;; only WHERE-VALUE and SRL are evaluated
118 (defmacro collect-umlisp-query ((table fields srl where-name where-value
119 &key (lrl "KCUILRL") distinct single
120 order like (query-cmd 'mutex-sql-query)
123 (let ((value (gensym))
126 (if (and limit (> limit 1))
127 (error "Can't set limit along with single.")
128 `(let* ((,value ,where-value)
129 (tuple (car (umlisp-query ,table ,fields ,srl ,where-name ,value
130 :lrl ,lrl :single ,single
131 :distinct ,distinct :order ,order
132 :like ,like :filter ,filter
133 :query-cmd ,query-cmd))))
134 ,@(unless where-name `((declare (ignore ,value))))
136 (destructuring-bind ,fields tuple
138 `(let ((,value ,where-value))
139 ,@(unless where-name `((declare (ignore ,value))))
141 (dolist (tuple (umlisp-query ,table ,fields ,srl ,where-name ,value
142 :lrl ,lrl :single ,single :distinct ,distinct
143 :order ,order :filter ,filter :like ,like
145 (push (destructuring-bind ,fields tuple ,@body) ,r))
149 (umlisp-query ,table ,fields ,srl ,where-name ,value
150 :lrl ,lrl :single ,single :distinct ,distinct
151 :order ,order :like ,like :filter ,filter :limit ,limit)
152 collect (destructuring-bind ,fields tuple ,@body))))))
154 (defmacro collect-umlisp-query-eval ((table fields srl where-name where-value
155 &key (lrl "KCUILRL") distinct single
156 order like filter limit)
158 (let ((value (gensym))
160 (eval-fields (cadr fields)))
162 `(let* ((,value ,where-value)
163 (tuple (car (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
164 :lrl ,lrl :single ,single
165 :distinct ,distinct :order ,order
166 :like ,like :filter ,filter
169 (destructuring-bind ,eval-fields tuple
171 `(let ((,value ,where-value)
173 (dolist (tuple (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
174 :lrl ,lrl :single ,single :distinct ,distinct
175 :order ,order :like ,like
176 :filter ,filter :limit ,limit))
177 (push (destructuring-bind ,eval-fields tuple ,@body) ,r))
181 (umlisp-query-eval ,table ,fields ,srl ,where-name ,value
182 :lrl ,lrl :single ,single :distinct ,distinct
183 :order ,order :like ,like :filter ,filter
185 collect (destructuring-bind ,eval-fields tuple ,@body))))))
188 ;;; Read from SQL database
190 (defmacro ensure-cui-integer (cui)
192 (setq ,cui (parse-cui ,cui))
195 (defmacro ensure-lui-integer (lui)
197 (setq ,lui (parse-lui ,lui))
200 (defmacro ensure-sui-integer (sui)
202 (setq ,sui (parse-sui ,sui))
205 (defmacro ensure-aui-integer (aui)
207 (setq ,aui (parse-aui ,aui))
210 (defmacro ensure-rui-integer (rui)
212 (setq ,rui (parse-rui ,rui))
215 (defmacro ensure-tui-integer (tui)
217 (setq ,tui (parse-tui ,tui))
220 (defmacro ensure-eui-integer (eui)
222 (setq ,eui (parse-eui ,eui))
225 (defun make-ucon-cui (cui)
226 (ensure-cui-integer cui)
228 (make-instance 'ucon :cui cui)))
230 (defun find-ucon-cui (cui &key (srl *current-srl*) without-pfstr)
231 "Find ucon for a cui. If set SAB, the without-pfstr is on by default"
232 (ensure-cui-integer cui)
233 (unless cui (return-from find-ucon-cui nil))
236 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :single t)
237 (make-instance 'ucon :cui cui :lrl (ensure-integer kcuilrl)
240 (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t :filter "KPFENG=1")
241 (make-instance 'ucon :cui cui :pfstr str
243 (collect-umlisp-query (mrconso (kcuilrl str) srl cui cui :single t)
244 (make-instance 'ucon :cui cui :pfstr str
247 (defun find-uconso-cui (cui &key sab (srl *current-srl*))
248 "Find uconso for a cui."
249 (ensure-cui-integer cui)
250 (unless cui (return-from find-uconso-cui nil))
252 (collect-umlisp-query (mrconso (lat ts lui stt sui ispref aui saui scui sdui sab tty code str
253 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
254 kluilrl ksuilrl) srl cui cui
255 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
256 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
257 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
258 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
259 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
262 (defun find-uconso-cuisui (cuisui &key sab (srl *current-srl*))
263 "Find uconso for a cuisui."
264 (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str
265 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
266 kluilrl ksuilrl) srl kcuisui cuisui
267 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
268 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
269 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
270 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
271 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
275 (defun find-uconso-code (code &key first sab (srl *current-srl*) (like nil))
276 "Return list of uconso objects that match code. Optional, filter for SAB. Optionally, use SQL's LIKE syntax"
277 (collect-umlisp-query (mrconso (cui sab) srl code code :like like :distinct t
279 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
280 (let ((uconsos (find-uconso-cui cui :sab sab :srl srl)))
285 (defun find-uconso-sui (sui &key sab (srl *current-srl*))
286 "Find uconso for a sui. If set SAB, the without-pfstr is on by default"
287 (ensure-sui-integer sui)
288 (unless (and sui (stringp sab))
289 (return-from find-uconso-sui nil))
291 (collect-umlisp-query (mrconso (cui lat ts lui stt sui ispref aui saui scui sdui sab tty code str
292 srl suppress cvf kpfeng kcuisui kcuilui kcuilrl
293 kluilrl ksuilrl) srl sui sui
295 :filter (if sab (concatenate 'string "SAB='" sab "'") nil))
296 (make-instance 'uconso :cui cui :lat lat :ts ts :lui lui :stt stt :sui sui :ispref ispref
297 :aui aui :saui saui :scui scui :sdui sdui :sab sab :tty tty :code code
298 :str str :srl srl :suppress suppress :cvf cvf :kpfeng kpfeng
299 :kcuisui kcuisui :kcuilui kcuilui :kcuilrl kcuilrl :kluilrl kluilrl
302 (defun find-pfstr-cui (cui &key (srl *current-srl*))
303 "Find preferred string for a cui"
304 (ensure-cui-integer cui)
306 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
307 :filter " KPFENG=1" :single t)
309 (collect-umlisp-query (mrconso (str) srl cui cui :distinct t
313 (defun find-lrl-cui (cui &key (srl *current-srl*))
315 (ensure-cui-integer cui)
316 (collect-umlisp-query (mrconso (kcuilrl) srl cui cui :distinct t :single t)
317 (ensure-integer kcuilrl)))
319 (defun find-ucon-lui (lui &key (srl *current-srl*))
320 "Find list of ucon for lui"
321 (ensure-lui-integer lui)
322 (unless lui (return-from find-ucon-lui nil))
324 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
325 :filter " KPFENG=1" :single t)
326 (make-instance 'ucon :cui (ensure-integer cui)
327 :pfstr str :lrl (ensure-integer kcuilrl)))
328 (collect-umlisp-query (mrconso (cui kcuilrl str) srl lui lui
330 (make-instance 'ucon :cui (ensure-integer cui)
331 :pfstr str :lrl (ensure-integer kcuilrl)))))
333 (defun find-ucon-sui (sui &key (srl *current-srl*))
334 "Find list of ucon for sui"
335 (ensure-sui-integer sui)
336 (collect-umlisp-query (mrconso (cui kcuilrl) srl sui sui :distinct t)
337 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
338 :lrl (ensure-integer kcuilrl))))
340 (defun find-ucon-aui (aui &key (srl *current-srl*))
341 "Find list of ucon for aui"
342 (ensure-aui-integer aui)
343 (collect-umlisp-query (mrconso (cui kcuilrl) srl aui aui :distinct t)
344 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
345 :lrl (ensure-integer kcuilrl))))
347 (defun find-ucon-cuisui (cuisui &key (srl *current-srl*))
348 "Find ucon for cui/sui"
349 (collect-umlisp-query (mrconso (cui kcuilrl) srl kcuisui cuisui)
350 (make-instance 'ucon :cui cui
351 :pfstr (find-pfstr-cui cui)
352 :lrl (ensure-integer kcuilrl))))
354 (defun find-ucon-cui-sui (cui sui &key (srl *current-srl*))
355 "Find ucon for cui/sui"
356 (ensure-cui-integer cui)
357 (ensure-sui-integer sui)
359 (find-ucon-cui-sui cui sui :srl srl)))
361 (defun find-ucon-str (str &key (srl *current-srl*))
362 "Find ucon that are exact match for str"
363 (collect-umlisp-query (mrconso (cui kcuilrl) srl str str :distinct t)
364 (make-instance 'ucon :cui (ensure-integer cui) :pfstr (find-pfstr-cui cui)
365 :lrl (ensure-integer kcuilrl))))
367 (defun find-ucon-all (&key (srl *current-srl*))
368 "Return list of all ucon's"
369 (with-sql-connection (db)
373 (destructuring-bind (cui cuilrl) tuple
374 (make-instance 'ucon :cui (ensure-integer cui)
375 :pfstr (find-pfstr-cui cui)
376 :lrl (ensure-integer cuilrl))))
377 (query-string mrconso (cui kcuilrl) srl nil nil
378 :order (cui asc) :distinct t)
381 (defun find-ucon-all2 (&key (srl *current-srl*))
382 "Return list of all ucon's"
383 (collect-umlisp-query (mrconso (cui kcuilrl) srl nil nil :order (cui asc)
385 (make-instance 'ucon :cui (ensure-integer cui)
386 :pfstr (find-pfstr-cui cui)
387 :lrl (ensure-integer kcuilrl))))
389 (defun find-cui-ucon-all (&key (srl *current-srl*))
390 "Return list of CUIs for all ucons"
391 (collect-umlisp-query (mrconso (cui) srl nil nil :order (cui asc)
395 (defun map-ucon-all (fn &key (srl *current-srl*))
396 "Map a function over all ucon's"
397 (with-sql-connection (db)
401 (destructuring-bind (cui cuilrl) tuple
402 (funcall fn (make-instance 'ucon :cui (ensure-integer cui)
403 :pfstr (find-pfstr-cui cui)
404 :lrl (ensure-integer cuilrl)))))
405 (query-string mrconso (cui kcuilrl) srl nil nil :order (cui asc)
410 (defun find-udef-cui (cui &key (srl *current-srl*))
411 "Return a list of udefs for cui"
412 (ensure-cui-integer cui)
413 (collect-umlisp-query (mrdef (sab def suppress) srl cui cui :lrl "KSRL")
414 (make-instance 'udef :sab sab :def def :suppress suppress)))
416 (defun find-udoc-key (key)
417 "Return list of abbreviation documentation for a key"
418 (collect-umlisp-query (mrdoc (value type expl) nil dockey key)
419 (make-instance 'udoc :dockey key :dvalue value :dtype type :expl expl)))
421 (defun find-udoc-value (value)
422 "Return abbreviation documentation"
423 (collect-umlisp-query (mrdoc (dockey type expl) nil value value)
424 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
426 (defun find-udoc-key-value (dockey value)
427 (collect-umlisp-query (mrdoc (type expl) nil dockey dockey :filter (format nil "VALUE='~A'" value))
428 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
430 (defun find-udoc-all ()
431 "Return all abbreviation documentation"
432 (collect-umlisp-query (mrdoc (dockey value type expl) nil nil nil)
433 (make-instance 'udoc :dockey dockey :dvalue value :dtype type :expl expl)))
435 (defun find-usty-cui (cui &key (srl *current-srl*))
436 "Return a list of usty for cui"
437 (ensure-cui-integer cui)
438 (collect-umlisp-query (mrsty (tui sty) srl cui cui :lrl "KLRL")
439 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
441 (defun find-usty-word (word &key (srl *current-srl*))
442 "Return a list of usty that match word"
443 (collect-umlisp-query (mrsty (tui sty) srl sty word :lrl klrl :like t
445 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
447 (defun find-urel-cui (cui &key (srl *current-srl*) filter without-pfstr2)
448 "Return a list of urel for cui"
449 (ensure-cui-integer cui)
450 (collect-umlisp-query (mrrel (aui1 rel stype1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
451 srl cui1 cui :lrl "KSRL" :filter filter)
453 (make-instance 'urel :cui1 cui :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
454 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
455 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
456 :suppress suppress :cvf cvf)))
457 (unless without-pfstr2
458 (setf (slot-value rel 'pfstr2) (find-pfstr-cui cui2)))
461 (defun find-urel-rui (rui &key (srl *current-srl*))
462 "Return the urel for a rui"
463 (ensure-rui-integer rui)
464 (collect-umlisp-query (mrrel (aui1 rel stype1 cui1 cui2 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
465 srl rui rui :lrl "KSRL" :single t)
466 (make-instance 'urel :cui1 cui1 :aui1 (ensure-integer aui1) :stype1 stype1 :rel rel
467 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2) :stype2 stype2
468 :rui (ensure-integer rui) :srui srui :rela rela :sab sab :sl sl :rg rg :dir dir
469 :suppress suppress :cvf cvf :pfstr2 (find-pfstr-cui cui2))))
471 (defun find-cui2-urel-cui (cui &key (srl *current-srl*))
472 "Return a list of urel for cui"
473 (ensure-cui-integer cui)
474 (collect-umlisp-query (mrrel (cui2) srl cui1
478 (defun find-urel-cui2 (cui2 &key (srl *current-srl*))
479 "Return a list of urel for cui2"
480 (ensure-cui-integer cui2)
481 (collect-umlisp-query (mrrel (rel cui1 aui1 stype1 aui2 stype2 rela rui srui sab sl rg dir suppress cvf)
482 srl cui2 cui2 :lrl "KSRL")
483 (make-instance 'urel :cui2 cui2 :rel rel :aui2 (ensure-integer aui2)
484 :stype2 stype2 :rui (ensure-integer rui) :srui srui
485 :stype1 stype1 :cui1 (ensure-integer cui1)
486 :aui1 (ensure-integer aui1)
487 :rela rela :sab sab :sl sl :rg rg :dir dir :suppress suppress :cvf cvf
488 :pfstr2 (find-pfstr-cui cui2))))
490 (defun find-ucon-rel-cui2 (cui2 &key (srl *current-srl*))
491 (ensure-cui-integer cui2)
492 (loop for cui in (remove-duplicates
493 (mapcar #'cui1 (find-urel-cui2 cui2 :srl srl)))
494 collect (find-ucon-cui cui :srl srl)))
496 (defun find-ucoc-cui (cui &key (srl *current-srl*))
497 "Return a list of ucoc for cui"
498 (ensure-cui-integer cui)
499 (collect-umlisp-query (mrcoc (aui1 cui2 aui2 sab cot cof coa) srl cui1
500 cui :lrl klrl :order (cof asc))
501 (setq cui2 (ensure-integer cui2))
502 (when (eql 0 cui2) (setq cui2 nil))
503 (make-instance 'ucoc :cui1 cui :aui1 (ensure-integer aui1)
504 :cui2 (ensure-integer cui2) :aui2 (ensure-integer aui2)
505 :cot cot :cof (ensure-integer cof) :coa coa :sab sab
506 :pfstr2 (find-pfstr-cui cui2))))
508 (defun find-ucoc-cui2 (cui2 &key (srl *current-srl*))
509 "Return a list of ucoc for cui2"
510 (ensure-cui-integer cui2)
511 (collect-umlisp-query (mrcoc (cui1 aui1 aui2 sab cot cof coa) srl cui2
512 cui2 :lrl klrl :order (cof asc))
513 (when (zerop cui2) (setq cui2 nil))
514 (make-instance 'ucoc :cui1 (ensure-integer cui1) :cui2 cui2
515 :aui1 (ensure-integer aui1) :aui2 (ensure-integer aui2)
516 :sab sab :cot cot :cof (ensure-integer cof) :coa coa
517 :pfstr2 (find-pfstr-cui cui2))))
519 (defun find-ucon-coc-cui2 (cui2 &key (srl *current-srl*))
520 "List of ucon with co-occurance cui2"
521 (ensure-cui-integer cui2)
523 #'(lambda (cui) (find-ucon-cui cui :srl srl))
524 (remove-duplicates (mapcar #'cui1 (find-ucoc-cui2 cui2 :srl srl)))))
527 (defun find-uterm-cui (cui &key (srl *current-srl*))
528 "Return a list of uterm for cui"
529 (ensure-cui-integer cui)
530 (collect-umlisp-query (mrconso (lui lat ts kluilrl) srl cui cui
531 :lrl kluilrl :distinct t)
532 (make-instance 'uterm :lui (ensure-integer lui) :cui cui
533 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
535 (defun find-uterm-lui (lui &key (srl *current-srl*))
536 "Return a list of uterm for lui"
537 (ensure-lui-integer lui)
538 (collect-umlisp-query (mrconso (cui lat ts kluilrl) srl lui lui
539 :lrl kluilrl :distinct t)
540 (make-instance 'uterm :cui (ensure-integer cui) :lui lui
541 :lat lat :ts ts :lrl (ensure-integer kluilrl))))
543 (defun find-uterm-cuilui (cui lui &key (srl *current-srl*))
544 "Return single uterm for cui/lui"
545 (ensure-cui-integer cui)
546 (ensure-lui-integer lui)
547 (collect-umlisp-query (mrconso (lat ts kluilrl) srl kcuilui
548 (make-cuilui cui lui)
549 :lrl kluilrl :single t)
550 (make-instance 'uterm :cui cui :lui lui :lat lat :ts ts
551 :lrl (ensure-integer kluilrl))))
553 (defun find-ustr-cuilui (cui lui &key (srl *current-srl*))
554 "Return a list of ustr for cui/lui"
555 (ensure-cui-integer cui)
556 (ensure-lui-integer lui)
557 (collect-umlisp-query (mrconso (sui stt str suppress ksuilrl) srl kcuilui
558 (make-cuilui cui lui) :lrl ksuilrl)
559 (make-instance 'ustr :sui (ensure-integer sui) :cui cui :lui lui
560 :cuisui (make-cuisui cui sui) :stt stt :str str :suppress suppress
561 :lrl (ensure-integer ksuilrl))))
563 (defun find-ustr-cuisui (cuisui &key (srl *current-srl*))
564 "Return the single ustr for cuisui"
565 (collect-umlisp-query (mrconso (cui lui sui stt str suppress ksuilrl) srl kcuisui
566 cuisui :lrl lsuilrl :single t)
567 (make-instance 'ustr :sui sui :cui cui :cuisui cuisui
568 :lui (ensure-integer lui) :stt stt :str str :suppress suppress
569 :lrl (ensure-integer ksuilrl))))
571 (defun find-ustr-cui-sui (cui sui &key (srl *current-srl*))
572 "Return the single ustr for cuisui"
573 (ensure-cui-integer cui)
574 (ensure-sui-integer sui)
575 (find-ustr-cuisui (make-cuisui cui sui) :srl srl))
577 (defun find-ustr-sui (sui &key (srl *current-srl*))
578 "Return the list of ustr for sui"
579 (ensure-sui-integer sui)
580 (collect-umlisp-query (mrconso (cui lui stt str suppress ksuilrl) srl sui sui
582 (make-instance 'ustr :sui sui :cui cui :stt stt :str str
583 :cuisui (make-cuisui (ensure-integer cui) sui)
585 :lui (ensure-integer lui) :lrl (ensure-integer ksuilrl))))
587 (defun find-ustr-sab (sab &key (srl *current-srl*))
588 "Return the list of ustr for sab"
589 (collect-umlisp-query (mrconso (kcuisui) srl sab sab :lrl srl)
590 (let ((cuisui (ensure-integer kcuisui)))
591 (find-ustr-cuisui cuisui :srl srl))))
593 (defun find-ustr-all (&key (srl *current-srl*))
594 "Return list of all ustr's"
595 (with-sql-connection (db)
599 (destructuring-bind (cui lui sui stt ksuilrl suppress) tuple
600 (make-instance 'ustr :cui (ensure-integer cui)
601 :lui (ensure-integer lui) :sui (ensure-integer sui)
602 :stt stt :str (find-pfstr-cui cui)
603 :cuisui (make-cuisui (ensure-integer cui)
604 (ensure-integer sui))
606 :lrl (ensure-integer ksuilrl))))
607 (query-string mrconso (cui lui sui stt ksuilrl) srl nil nil :lrl ksuilrl
612 (defun find-string-sui (sui &key (srl *current-srl*))
613 "Return the string associated with sui"
614 (ensure-sui-integer sui)
615 (collect-umlisp-query (mrconso (str) srl sui sui :lrl ksuilrl :single t)
618 (defun find-uso-cuisui (cui sui &key (srl *current-srl*))
619 (ensure-sui-integer sui)
620 (ensure-cui-integer cui)
621 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str ts)
622 srl kcuisui (make-cuisui cui sui) :lrl srl)
623 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
624 :cui cui :sui sui :saui saui :sdui sdui :scui scui
625 :lat lat :str str :ts ts)))
627 (defun find-uso-cui (cui &key (srl *current-srl*) (english-only nil) limit)
628 (ensure-cui-integer cui)
629 (collect-umlisp-query (mrconso (aui sab code srl tty saui sdui scui lat str sui ts)
630 srl cui cui :lrl srl :limit limit
631 :filter (when english-only "LAT='ENG'"))
632 (make-instance 'uso :aui aui :sab sab :code code :srl srl :tty tty
633 :cui cui :sui sui :saui saui :sdui sdui :scui scui
634 :lat lat :str str :ts ts)))
636 (defun find-uso-aui (aui &key (srl *current-srl*))
637 (ensure-sui-integer aui)
638 (collect-umlisp-query (mrconso (sab cui sui code srl tty saui sdui scui lat
639 str ts) srl aui aui :lrl srl :single t)
640 (make-instance 'uso :aui aui :cui cui :sab sab :code code :srl srl :tty tty
641 :sui sui :saui saui :sdui sdui :scui scui :lat lat
644 (defun find-uhier-cui (cui &key (srl *current-srl*))
645 (ensure-cui-integer cui)
646 (collect-umlisp-query (mrhier (aui cxn paui sab rela ptr hcd cvf)
647 srl cui cui :lrl ksrl)
648 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
649 :cxn (ensure-integer cxn)
650 :paui (ensure-integer paui)
651 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
653 (defun find-uhier-all (&key (srl *current-srl*))
654 (collect-umlisp-query (mrhier (cui aui cxn paui sab rela ptr hcd cvf)
655 srl nil nil :lrl ksrl)
656 (make-instance 'uhier :cui cui :aui (ensure-integer aui)
657 :cxn (ensure-integer cxn)
658 :paui (ensure-integer paui)
659 :sab sab :rela rela :ptr ptr :hcd hcd :cvf cvf)))
661 (defun find-usat-ui (cui &optional lui sui &key (srl *current-srl*))
662 (ensure-cui-integer cui)
663 (ensure-lui-integer lui)
664 (ensure-sui-integer sui)
665 (let ((ls "SELECT CODE,ATN,SAB,ATV FROM MRSAT WHERE "))
667 (sui (string-append ls "KCUISUI='"
668 (integer-string (make-cuisui cui sui) 14)
670 (lui (string-append ls "KCUILUI='"
671 (integer-string (make-cuilui cui lui) 14)
673 (t (string-append ls "cui='" (prefixed-fixnum-string cui nil 7)
674 "' and lui='0' and sui='0'")))
676 (string-append ls " and KSRL<=" (prefixed-fixnum-string srl nil 3)))
677 (loop for tuple in (mutex-sql-query ls) collect
678 (destructuring-bind (code atn sab atv) tuple
679 (make-instance 'usat :code code :atn atn :sab sab :atv atv)))))
681 (defun find-usty-tui (tui)
683 (ensure-tui-integer tui)
684 (collect-umlisp-query (mrsty (sty) nil tui tui :single t)
685 (make-instance 'usty :tui tui :sty sty)))
687 (defun find-usty-sty (sty)
688 "Find usty for a sty"
689 (collect-umlisp-query (mrsty (tui) nil sty sty :single t)
690 (make-instance 'usty :tui (ensure-integer tui) :sty sty)))
692 (defun find-usty-all ()
693 "Return list of usty's for all semantic types"
694 (collect-umlisp-query (mrsty (tui) nil nil nil :distinct t)
695 (find-usty-tui tui)))
697 (defun find-usab-all ()
698 "Return all usab objects"
699 (collect-umlisp-query (mrsab (vcui rcui vsab rsab son sf sver vstart vend imeta
700 rmeta slc scc srl tfr cfr cxty ttyl atnl lat
701 cenc curver sabin ssn scit) nil nil nil)
702 (make-instance 'usab :vcui (ensure-integer vcui)
703 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
704 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
705 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
706 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
707 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
708 :curver curver :sabin sabin :ssn ssn :scit scit)))
710 (defun find-usab-by-key (key-name key &key current)
711 "Find usab for a key"
712 (collect-umlisp-query-eval ('mrsab '(vcui rcui vsab rsab son sf sver vstart
713 vend imeta rmeta slc scc srl tfr cfr cxty
714 ttyl atnl lat cenc curver sabin
716 nil key-name key :single t
717 :filter (when current "RMETA=''"))
718 (make-instance 'usab :vcui (ensure-integer vcui)
719 :rcui (ensure-integer rcui) :vsab vsab :rsab rsab :son son
720 :sf sf :sver sver :vstart vstart :vend vend :imeta imeta
721 :rmeta rmeta :slc slc :scc scc :srl (ensure-integer srl)
722 :tfr (ensure-integer tfr) :cfr (ensure-integer cfr)
723 :cxty cxty :ttyl ttyl :atnl atnl :lat lat :cenc cenc
724 :curver curver :sabin sabin
725 :ssn ssn :scit scit)))
727 (defun find-usab-rsab (rsab &key (current t))
729 (find-usab-by-key 'rsab rsab))
731 (defun find-usab-vsab (vsab &key (current t))
733 (find-usab-by-key 'vsab vsab))
735 (defun find-cui-max ()
736 (ensure-integer (caar (mutex-sql-query "select max(CUI) from MRCON"))))
738 (defun find-umap-cui (cui)
739 (ensure-cui-integer cui)
740 (collect-umlisp-query (mrmap (mapsetsab mapsubsetid maprank fromid fromsid fromexpr
741 fromtype fromrule fromres rel rela toid tosid
742 toexpr totype torule tores maprule maptype
745 (make-instance 'umap :mapsetcui cui :mapsetsab mapsetsab :mapsubsetid mapsubsetid
746 :maprank (ensure-integer maprank) :fromid fromid :fromsid fromsid
747 :fromexpr fromexpr :fromtype fromtype :fromrule fromrule :fromres fromres
748 :rel rel :rela rela :toid toid :tosid tosid :toexpr toexpr :totype totype
749 :torule torule :tores tores :maprule maprule :maptype maptype :mapatn mapatn
750 :mapatv mapatv :cvf cvf)))
752 (defun find-usmap-cui (cui)
753 (ensure-cui-integer cui)
754 (collect-umlisp-query (mrsmap (mapsetsab fromexpr fromtype rel rela toexpr totype cvf)
756 (make-instance 'usmap :mapsetcui cui :mapsetsab mapsetsab
757 :fromexpr fromexpr :fromtype fromtype
758 :rel rel :rela rela :toexpr toexpr :totype totype
761 ;;;; Cross table find functions
763 (defun find-ucon-tui (tui &key (srl *current-srl*))
764 "Find list of ucon for tui"
765 (ensure-tui-integer tui)
766 (collect-umlisp-query (mrsty (cui) srl tui tui :lrl klrl :order (cui asc))
767 (find-ucon-cui (ensure-integer cui) :srl srl)))
769 (defun mrconso-query-word-cui (word sab srl like)
770 (format nil "SELECT DISTINCT c.cui FROM MRCONSO c,MRXW_ENG x WHERE x.WD~A'~A' AND x.cui=c.cui~A~A"
771 (if like " LIKE " "=")
772 (clsql-sys::sql-escape-quotes word)
775 (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
777 (format nil " AND c.sab IN (~{'~A'~^,~})"
778 (mapcar 'clsql-sys::sql-escape-quotes sab)))
781 (if srl (format nil " AND KCUILRL <= ~A" srl) "")))
783 (defun mrconso-query-word-sui (word sab srl like)
784 (format nil "SELECT DISTINCT c.sui FROM MRCONSO c,MRXW_ENG x WHERE x.WD~A'~A' AND x.sui=c.sui~A~A"
785 (if like " LIKE " "=")
786 (clsql-sys::sql-escape-quotes word)
789 (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
791 (format nil " AND c.sab IN (~{'~A'~^,~})"
792 (mapcar 'clsql-sys::sql-escape-quotes sab)))
795 (if srl (format nil " AND KCUILRL <= ~A" srl) "")))
797 (defun find-uconso-word (word &key sab (srl *current-srl*) (like nil))
798 "Return list of uconso that match word. Optionally, matching SAB. Optionally, use SQL's LIKE syntax"
801 (let ((sui-query (mrconso-query-word-sui word sab srl like))
803 (dolist (sui (remove-duplicates (sort (mapcar 'car (mutex-sql-query sui-query)) #'<)))
804 (setq uconsos (nconc uconsos (find-uconso-sui sui :sab sab))))
805 (remove-duplicates uconsos :key 'cui)))
807 (collect-umlisp-query-eval ('mrxw_eng '(kcuisui) srl 'wd word :like like
808 :lrl 'klrl :order '(kcuisui asc))
809 (find-uconso-cuisui kcuisui :srl srl)))))
811 (defun find-ucon-word (word &key sab (srl *current-srl*) (like nil))
812 "Return list of ucon that match word in matching SAB. Optionally, use SQL's LIKE syntax"
815 (let ((query (mrconso-query-word-cui word sab srl like)))
816 (loop for tuple in (mutex-sql-query query)
817 collect (make-instance 'ucon :cui (first tuple)))))
819 (collect-umlisp-query-eval ('mrxw_eng '(cui) srl 'wd word :like like :distinct t
820 :lrl 'klrl :order '(cui asc))
821 (find-ucon-cui cui :srl srl)))))
823 (defun find-ucon-normalized-word (word &key (srl *current-srl*) (like nil))
824 "Return list of ucons that match word, optionally use SQL's LIKE syntax"
825 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
826 :lrl 'klrl :order '(cui asc))
827 (find-ucon-cui cui :srl srl)))
829 (defun find-cui-normalized-word (word &key (srl *current-srl*) (like nil))
830 "Return list of cui that match word, optionally use SQL's LIKE syntax"
831 (collect-umlisp-query-eval ('mrxnw_eng '(cui) srl 'nwd word :like like :distinct t
832 :lrl 'klrl :order '(cui asc))
835 (defun find-lui-normalized-word (word &key (srl *current-srl*) (like nil))
836 "Return list of cui that match word, optionally use SQL's LIKE syntax"
837 (collect-umlisp-query-eval ('mrxnw_eng '(lui) srl 'nwd word :like like :distinct t
838 :lrl 'klrl :order '(cui asc))
841 (defun find-sui-normalized-word (word &key (srl *current-srl*) (like nil))
842 "Return list of cui that match word, optionally use SQL's LIKE syntax"
843 (collect-umlisp-query-eval ('mrxnw_eng '(sui) srl 'nwd word :like like :distinct t
844 :lrl 'klrl :order '(cui asc))
847 (defun find-ustr-word (word &key sab (srl *current-srl*) (like nil))
848 "Return list of ustr that match word in matching SAB. Optionally, use SQL's LIKE syntax"
851 (let ((query (format nil "SELECT c.sui,c.cui,c.lui,c.str,c.lrl,c.stt,c.suppress,c.cuisui FROM MRCONSO c,MRXW_ENG x WHERE x.WD ~A '~A' AND x.cui=c.cui AND x.lui=c.lui AND x.sui=c.sui~A~A"
853 (clsql-sys::sql-escape-quotes word)
856 (format nil " AND c.sab='~A'" (clsql-sys::sql-escape-quotes sab)))
858 (format nil " AND c.sab IN (~('~A'~^,~))"
859 (mapcar 'clsql-sys::sql-escape-quotes sab)))
862 (if srl (format nil " AND KCUILRL <= ~D" srl) ""))))
863 (loop for tuple in (mutex-sql-query query)
864 collect (destructuring-bind (sui cui lui str lrl stt suppress cuisui) tuple
865 (make-instance 'ustr :sui sui :cui cui :lui lui :str str :lrl lrl
866 :stt stt :suppress suppress :cuisui cuisui)))))
868 (collect-umlisp-query (mrxw_eng (kcuisui) srl wd word :lrl klrl
869 :order (cui asc sui asc))
870 (find-ustr-cuisui kcuisui :srl srl)))))
872 (defun find-ustr-normalized-word (word &key (srl *current-srl*))
873 "Return list of ustrs that match word"
874 (collect-umlisp-query (mrxnw_eng (kcuisui) srl nwd word :lrl klrl
875 :order (cui asc sui asc))
876 (find-ustr-cuisui kcuisui :srl srl)))
878 (defun find-uterm-word (word &key (srl *current-srl*))
879 "Return list of uterms that match word"
880 (collect-umlisp-query (mrxw_eng (cui lui) srl wd word :lrl klrl
881 :order (cui asc lui asc))
882 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
884 (defun find-uterm-normalized-word (word &key (srl *current-srl*))
885 "Return list of uterms that match word"
886 (collect-umlisp-query (mrxnw_eng (cui lui) srl nwd word :lrl klrl
887 :order (cui asc lui asc))
888 (find-uterm-cuilui (ensure-integer cui) (ensure-integer lui) :srl srl)))
890 (defun find-ucon-noneng-word (word &key (srl *current-srl*) (like nil))
891 "Return list of ucons that match non-english word"
892 (collect-umlisp-query-eval ('mrxw_noneng '(cui) srl 'wd word :like like
893 :distinct t :lrl 'klrl :order '(cui asc))
894 (find-ucon-cui cui :srl srl)))
896 (defun find-ustr-noneng-word (word &key (srl *current-srl*))
897 "Return list of ustrs that match non-english word"
898 (collect-umlisp-query (mrxw_noneng (kcuisui) srl wd word :lrl klrl
899 :order (cui asc sui asc))
900 (find-ustr-cuisui kcuisui :srl srl)))
904 (defun find-usrl-all ()
905 (collect-umlisp-query (usrl (sab srl) nil nil nil :order (sab asc))
906 (make-instance 'usrl :sab sab :srl (ensure-integer srl))))
908 ;;; Multiword lookup and score functions
910 (defun find-uobj-multiword (str obj-lookup-fun sort-fun key srl
911 only-exact-if-match limit &key extra-lookup-args)
913 (dolist (word (delimited-string-to-list str #\space))
914 (setq uobjs (nconc uobjs
915 (kmrcl:flatten (apply obj-lookup-fun word :srl srl extra-lookup-args)))))
917 (funcall sort-fun str
918 (delete-duplicates uobjs :test #'= :key key))))
919 (let ((len (length sorted)))
922 (return-from find-uobj-multiword nil))
923 ((and only-exact-if-match (multiword-match str (pfstr (first sorted))))
926 (if (and (plusp limit) (> len limit))
927 (subseq sorted 0 limit)
932 (defun find-ucon-multiword (str &key (srl *current-srl*)
933 (only-exact-if-match t)
936 (find-uobj-multiword str #'find-ucon-word #'sort-score-pfstr-str
937 #'cui srl only-exact-if-match limit
938 :extra-lookup-args (list :sab sab)))
940 (defun find-uconso-multiword (str &key (srl *current-srl*)
941 (only-exact-if-match t)
944 (find-uobj-multiword str #'find-uconso-word #'sort-score-pfstr-str
945 #'cui srl only-exact-if-match limit
946 :extra-lookup-args (list :sab sab)))
948 (defun find-uterm-multiword (str &key (srl *current-srl*)
949 (only-exact-if-match t)
951 (find-uobj-multiword str #'find-uterm-word #'sort-score-pfstr-str
952 #'lui srl only-exact-if-match limit))
954 (defun find-ustr-multiword (str &key (srl *current-srl*)
955 (only-exact-if-match t)
958 (find-uobj-multiword str #'find-ustr-word #'sort-score-ustr-str
959 #'sui srl only-exact-if-match limit
960 :extra-lookup-args (list :sab sab)))
962 (defun sort-score-pfstr-str (str uobjs)
963 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
964 (sort-score-umlsclass-str uobjs str #'pfstr))
966 (defun sort-score-ustr-str (str ustrs)
967 "Return list of sorted and scored ucons. Score by match of str to ucon-pfstr"
968 (sort-score-umlsclass-str ustrs str #'str))
970 (defun sort-score-umlsclass-str (objs str lookup-func)
971 "Sort a list of objects based on scoring to a string"
974 (push (list obj (score-multiword-match str (funcall lookup-func obj)))
976 (mapcar #'car (sort scored #'> :key #'cadr))))
979 ;;; LEX SQL functions
981 (defun find-lexterm-eui (eui)
982 (ensure-eui-integer eui)
983 (collect-umlisp-query (lrwd (wrd) nil eui eui :single t)
984 (make-instance 'lexterm :eui eui :wrd wrd)))
986 (defun find-lexterm-word (wrd)
987 (collect-umlisp-query (lrwd (eui) nil wrd wrd)
988 (make-instance 'lexterm :eui (ensure-integer eui)
989 :wrd (copy-seq wrd))))
991 ;; LEX SQL Read functions
993 (defun find-labr-eui (eui)
994 (ensure-eui-integer eui)
995 (collect-umlisp-query (lrabr (bas abr eui2 bas2) nil eui eui)
996 (make-instance 'labr :eui eui :bas bas :abr abr :bas2 bas2
997 :eui2 (ensure-integer eui2))))
999 (defun find-labr-bas (bas)
1000 (collect-umlisp-query (labr (eui abr eui2 bas2) nil bas bas)
1001 (make-instance 'labr :eui (ensure-integer eui) :abr abr :bas2 bas2
1002 :bas (copy-seq bas) :eui2 (ensure-integer eui2))))
1004 (defun find-lagr-eui (eui)
1005 (ensure-eui-integer eui)
1006 (collect-umlisp-query (lragr (str sca agr cit bas) nil eui eui)
1007 (make-instance 'lagr :eui eui :str str :sca sca :agr agr
1008 :cit cit :bas bas)))
1010 (defun find-lcmp-eui (eui)
1011 (ensure-eui-integer eui)
1012 (collect-umlisp-query (lrcmp (bas sca com) nil eui eui)
1013 (make-instance 'lcmp :eui eui :bas bas :sca sca :com com)))
1015 (defun find-lmod-eui (eui)
1016 (ensure-eui-integer eui)
1017 (collect-umlisp-query (lrmod (bas sca psn_mod fea) nil eui eui)
1018 (make-instance 'lmod :eui eui :bas bas :sca sca :psnmod psn_mod :fea fea)))
1020 (defun find-lnom-eui (eui)
1021 (ensure-eui-integer eui)
1022 (collect-umlisp-query (lrnom (bas sca eui2 bas2 sca2) nil eui eui)
1023 (make-instance 'lnom :eui eui :bas bas :sca sca :bas2 bas2 :sca2 sca2
1024 :eui2 (ensure-integer eui2))))
1026 (defun find-lprn-eui (eui)
1027 (ensure-eui-integer eui)
1028 (collect-umlisp-query (lrprn (bas num gnd cas pos qnt fea) nil eui eui)
1029 (make-instance 'lprn :eui eui :bas bas :num num :gnd gnd
1030 :cas cas :pos pos :qnt qnt :fea fea)))
1032 (defun find-lprp-eui (eui)
1033 (ensure-eui-integer eui)
1034 (collect-umlisp-query (lrprp (bas str sca fea) nil eui eui)
1035 (make-instance 'lprp :eui eui :bas bas :str str :sca sca :fea fea)))
1037 (defun find-lspl-eui (eui)
1038 (ensure-eui-integer eui)
1039 (collect-umlisp-query (lrspl (spv bas) nil eui eui)
1040 (make-instance 'lspl :eui eui :spv spv :bas bas)))
1042 (defun find-ltrm-eui (eui)
1043 (ensure-eui-integer eui)
1044 (collect-umlisp-query (lrtrm (bas gen) nil eui eui)
1045 (make-instance 'ltrm :eui eui :bas bas :gen gen)))
1047 (defun find-ltyp-eui (eui)
1048 (ensure-eui-integer eui)
1049 (collect-umlisp-query (lrtyp (bas sca typ) nil eui eui)
1050 (make-instance 'ltyp :eui eui :bas bas :sca sca :typ typ)))
1052 (defun find-lwd-wrd (wrd)
1053 (make-instance 'lwd :wrd wrd
1054 :euilist (collect-umlisp-query (lrwd (eui) nil wrd wrd)
1055 (ensure-integer eui))))
1057 ;;; Semantic Network SQL access functions
1059 (defun find-sdef-ui (ui)
1060 (collect-umlisp-query (srdef (rt sty_rl stn_rtn def ex un rh abr rin)
1061 nil ui ui :single t)
1062 (make-instance 'sdef :rt rt :ui ui :styrl sty_rl :stnrtn stn_rtn
1063 :def def :ex ex :un un :rh rh :abr abr :rin rin)))
1065 (defun find-sstre1-ui (ui)
1066 (collect-umlisp-query (srstre1 (ui2 ui3) nil ui ui)
1067 (make-instance 'sstre1 :ui ui :ui2 (ensure-integer ui2)
1068 :ui3 (ensure-integer ui3))))
1070 (defun find-sstre1-ui2 (ui2)
1071 (collect-umlisp-query (srstre1 (ui ui3) nil ui2 ui2)
1072 (make-instance 'sstre1 :ui (ensure-integer ui) :ui2 ui2
1073 :ui3 (ensure-integer ui3))))
1075 (defun find-sstr-rl (rl)
1076 (collect-umlisp-query (srstre (sty_rl sty_rl2 ls) nil rl rl)
1077 (make-instance 'sstr :rl rl :styrl sty_rl :styrl2 sty_rl2 :ls ls)))
1079 (defun find-sstre2-sty (sty)
1080 (collect-umlisp-query (srstre2 (rl sty2) nil sty sty)
1081 (make-instance 'sstre2 :sty (copy-seq sty) :rl rl :sty2 sty2)))
1083 (defun find-sstr-styrl (styrl)
1084 (collect-umlisp-query (srstr (rl sty_rl2 ls) nil styrl styrl)
1085 (make-instance 'sstr :styrl styrl :rl rl :styrl2 sty_rl2 :ls ls)))
1088 ;;; **************************
1090 ;;; **************************
1093 (defun make-ustats ()
1094 (with-sql-connection (conn)
1095 (ignore-errors (sql-execute "drop table USTATS" conn))
1096 (sql-execute "create table USTATS (NAME varchar(160), COUNT bigint, SRL integer)" conn)
1098 (dolist (srl '(0 1 2 3 4 9))
1099 (insert-ustats-count conn "Concept Count" "MRCONSO" "distinct CUI" "KCUILRL" srl)
1100 (insert-ustats-count conn "Term Count" "MRCONSO" "distinct KCUILUI" "KCUILRL" srl)
1101 (insert-ustats-count conn "Distinct Term Count" "MRCONSO" "distinct LUI" "KLUILRL" srl)
1102 (insert-ustats-count conn "String Count" "MRCONSO" "*" "KSUILRL" srl)
1103 (insert-ustats-count conn "Distinct String Count" "MRCONSO" "distinct SUI" "KSUILRL" srl)
1104 (insert-ustats-count conn "Hierarchcy" "MRHIER" "*" "KSRL" srl)
1105 (insert-ustats-count conn "Mappings" "MRMAP" "*" "KSRL" srl)
1106 (insert-ustats-count conn "Simple Mappings" "MRSMAP" "*" "KSRL" srl)
1107 (insert-ustats-count conn "Co-occuring Concept Count" "MRCOC" "*" "KLRL" srl)
1108 (insert-ustats-count conn "Definition Count" "MRDEF" "*" "KSRL" srl)
1109 (insert-ustats-count conn "Rank Count" "MRRANK" "*" "KSRL" srl)
1110 (insert-ustats-count conn "Relationship Count" "MRREL" "*" "KSRL" srl)
1111 (insert-ustats-count conn "Semantic Type Count" "MRSTY" "*" "KLRL" srl)
1112 (insert-ustats-count conn "Simple Attribute Count" "MRSAT" "*" "KSRL" srl)
1113 (insert-ustats-count conn "Source Abbreviation Count" "MRSAB" "*" "SRL" srl)
1114 (insert-ustats-count conn "Word Index Count" "MRXW_ENG" "*" "KLRL" srl)
1115 (insert-ustats-count conn "Normalized Word Index Count" "MRXNW_ENG" "*" "KLRL" srl)
1116 (insert-ustats-count conn "Normalized String Index Count" "MRXNS_ENG" "*" "KLRL" srl))
1117 (sql-execute "create index USTATS_SRL on USTATS (SRL)" conn))
1120 (defun insert-ustats-count (conn name table count-variable srl-control srl)
1121 (insert-ustats conn name (find-count-table conn table srl count-variable srl-control) srl))
1123 (defun find-count-table (conn table srl count-variable srl-control)
1125 ((stringp srl-control)
1127 (caar (sql-query (format nil "select count(~a) from ~a where ~a <= ~d"
1128 count-variable table srl-control srl)
1132 (caar (sql-query (format nil "select count(~a) from ~a"
1133 count-variable table )
1136 (error "Unknown srl-control")
1139 (defun insert-ustats (conn name count srl)
1140 (sql-execute (format nil "insert into USTATS (name,count,srl) values ('~a',~d,~d)"
1141 name count (if srl srl 3))
1144 (defun find-ustats-all (&key (srl *current-srl*))
1146 (collect-umlisp-query (ustats (name count srl) nil srl srl
1148 (make-instance 'ustats :name name
1149 :hits (ensure-integer count)
1150 :srl (ensure-integer srl)))
1151 (collect-umlisp-query (ustats (name count srl) nil nil nil
1153 (make-instance 'ustats :name name
1154 :hits (ensure-integer count)
1155 :srl (ensure-integer srl)))))
1157 (defun find-ustats-srl (srl)
1158 (collect-umlisp-query (ustats (name count) nil srl srl :order (name asc))
1159 (make-instance 'ustats :name name :hits (ensure-integer count))))